We have performed embedded-cluster calculations using density functional theory to investigate mechanisms of nitrogen substitution (nitridation) in HY and silicalite zeolites. We consider nitridation as replacing Si–O–Si and Si–OH–Al linkages with Si–NH–Si and Si–NH 2–Al, respectively. We predict that nitridation is much less endothermic in HY (29 kJ/mol) than in silicalite (132 kJ/mol), indicating the possibility of higher nitridation yields in HY. To reveal mechanistic details, we have combined for the first time the nudged elastic band method of finding elusive transition states, with the ONIOM method of treating embedded quantum clusters. We predict that nitridation of silicalite proceeds via a planar intermediate involving a ▪ ring with pentavalent Si, whereas nitridation of HY is found to proceed via an intermediate similar to physisorbed ammonia. B3LYP/6-311G(d,p) calculations give an overall barrier for silicalite nitridation of 343 kJ/mol, while that in HY is 359 kJ/mol. Although the overall nitridation barriers are relatively high, requiring high temperatures for substitution, the overall barriers for the reverse processes are also high. As such, we predict that once these catalysts are made, they remain relatively stable.